Upgrade to Keras 3.9

[LarsKue]

We need this upgrade to get rid of a security vulnerability in Keras < 3.9:

https://nvd.nist.gov/vuln/detail/CVE-2025-1550
GHSA-48g7-3x6r-xfhp

[LarsKue]

Looks like 3.9.0 is not available yet on conda-forge. We should probably update our CI install pipeline to rely on pip rather than conda.

[LarsKue]

There are some errors still that are subject to be fixed by #350.

[stefanradev93]

Strange, there seems to be a problem with serializing the scores even though everything used to work for < 3.9.

[codecov-commenter]

⚠️ Please install the to ensure uploads and comments are reliably processed by Codecov.

Codecov Report

Attention: Patch coverage is 70.27027% with 11 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
...w/networks/consistency_models/consistency_model.py	0.00%	3 Missing ⚠️
bayesflow/links/ordered_quantiles.py	50.00%	2 Missing ⚠️
bayesflow/networks/embeddings/fourier_embedding.py	0.00%	2 Missing ⚠️
bayesflow/scores/multivariate_normal_score.py	71.42%	2 Missing ⚠️
bayesflow/links/ordered.py	66.66%	1 Missing ⚠️
bayesflow/utils/_docs/_populate_all.py	50.00%	1 Missing ⚠️

❗ Your organization needs to install the Codecov GitHub app to enable full functionality.

Files with missing lines	Coverage Δ
bayesflow/adapters/transforms/as_set.py	93.75% <100.00%> (ø)
bayesflow/adapters/transforms/sqrt.py	85.71% <100.00%> (ø)
bayesflow/links/positive_semi_definite.py	100.00% <100.00%> (ø)
bayesflow/scores/mean_score.py	100.00% <100.00%> (ø)
bayesflow/scores/median_score.py	100.00% <100.00%> (ø)
bayesflow/scores/normed_difference_score.py	100.00% <100.00%> (ø)
bayesflow/scores/parametric_distribution_score.py	86.66% <100.00%> (+2.05%)	⬆️
bayesflow/scores/quantile_score.py	100.00% <100.00%> (ø)
bayesflow/scores/scoring_rule.py	91.30% <100.00%> (+0.39%)	⬆️
bayesflow/links/ordered.py	96.87% <66.66%> (-3.13%)	⬇️
... and 5 more

... and 3 files with indirect coverage changes

🚀 New features to boost your workflow:

• ❄ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.